You mean when going online and RSLogix wants to merge the online program with an offline project.
The smartest is to do an offline/online compare of the complete project. That will tell you how big the differences are between the offline and the online projects.
If the differences are minor, then I always simply recreate the differences in the offline project. That keeps the network comments in the right place. If complete networks have been inserted, you can simply copy-paste from online to offline.
If there are blocks that are totrally different or missing offline, you can upload only these blocks. Network comments will then have to put in anew, after analysing what the code does.